WASHINGTON, April 3  Jose Padilla, the American citizen
held for more than three years in military custody as an enemy
combatant, fell one vote short on Monday of persuading the Supreme
Court to take his case.

Four votes are necessary for the court to take a case, and
Mr. Padilla's appeal received only three. The result was to leave
standing a decision by the federal appeals court in Richmond,
Va., that endorsed the government's power to seize a citizen
on United States soil and keep him in open-ended detention.

Nonetheless, the outcome was not the unalloyed victory for
the Bush administration that it might have appeared to be.

Three justices who voted not to hear the case  Justices
Anthony M. Kennedy and John Paul Stevens, along with Chief Justice
John G. Roberts Jr.  filed an unusual opinion explaining
their position. They noted that Mr. Padilla, who is now out of
military custody and awaiting trial in federal district court
in Miami on terrorism-related charges, was entitled to a criminal
defendant's full range of protections, including the right to
a speedy trial.

Most significant, the three justices warned the administration
that the federal courts, including the Supreme Court, stood ready
to intervene "were the government to seek to change the
status or conditions of Padilla's custody."

The comment was clearly a reference to the sequence of events
last fall, when the administration, days before it was due to
file a brief in response to Mr. Padilla's Supreme Court appeal,
announced that it had obtained a grand jury indictment and planned
to shift him to civilian custody.

The administration then filed a brief arguing that the appeal
had to be dismissed as moot, since Mr. Padilla was getting the
relief he requested when he filed his original petition asking
to be released from custody or charged with a crime.

The Miami indictment charges him with providing material support
to terrorists as part of a cell that is said to have sent money
and recruits overseas. He is being held without bail; a trial
is scheduled for Sept. 9.

In simply turning down Mr. Padilla's appeal, Padilla v. Hanft,
No. 05-533, the court did not make a formal determination that
the case was moot. But Mr. Padilla's transfer from military custody
to the civilian justice system rendered his legal claims, "at
least for now, hypothetical," Justice Kennedy said in the
explanatory opinion, which the two other justices signed.

"Even if the court were to rule in Padilla's favor, his
present custody status would be unaffected," Justice Kennedy
said.

In shifting Mr. Padilla to civilian custody, the government
said that it reserved the right to redesignate him as an enemy
combatant and send him back to military custody. His lawyers
argued that for that reason, the Supreme Court should hear his
case.

Justice Ruth Bader Ginsburg agreed, filing an opinion on Monday
dissenting from the court's refusal to hear the case.

"Nothing the government has yet done purports to retract
the assertion of executive power Padilla protests," Justice
Ginsburg said, adding that "nothing prevents the executive
from returning to the road it earlier constructed and defended."
She said she was "satisfied that this case is not moot."

Justices David H. Souter and Stephen G. Breyer did not sign
Justice Ginsburg's opinion, noting only that they, too, had voted
to hear the case.

Justices Antonin Scalia, Clarence Thomas and Samuel A. Alito
Jr., who voted against hearing the appeal, neither signed Justice
Kennedy's opinion nor offered an explanation of their own. It
is possible that they objected to the language in the Kennedy
opinion about the court's readiness to intervene "promptly
to ensure that the office and purposes of the writ of habeas
corpus are not compromised" if the administration were to
change Mr. Padilla's status once again.

The silence of these three justices was only one of several
mysteries surrounding the court's disposition of the case, among
the most prominent of the cases generated by the administration's
handling of those it has labeled enemy combatants.

One mystery is what took the court so long. Mr. Padilla's
appeal had been pending for months, and had been taken up by
the justices at their weekly closed-door conference eight times
since mid-January. That length of time was hardly needed to produce
the four pages of opinions, three for Justice Kennedy and one
for Justice Ginsburg, that the court issued on Monday.

Another mystery is the role played by Justice Stevens, who
signed Justice Kennedy's opinion rather than provide a crucial
fourth vote to his natural allies  Justices Ginsburg, Souter
and Breyer. Two years ago, Justice Stevens wrote for Justices
Ginsburg, Souter and Breyer in dissent from an earlier ruling
in Mr. Padilla's legal saga.

That was a 5-to-4 decision holding that the federal appeals
court in New York, which had ordered Mr. Padilla released, lacked
the authority to decide the case. The five justices in the majority
then required Mr. Padilla to file a new habeas corpus petition
seeking release in South Carolina, where he was held in the Navy
brig in Charleston.

Justice Stevens, dissenting, criticized the majority as failing
to address the merits of Mr. Padilla's case, which he said "raises
questions of profound importance to the nation."

In her dissenting opinion on Monday, Justice Ginsburg quoted
those words, identifying them as those of Justice Stevens. As
a careful writer, not given to wasting words herself, Justice
Ginsburg appeared to be sending a signal of her dismay at Justice
Stevens's failure to join her in dissent this time.

The two mysteries  the lengthy consideration and the
role of Justice Stevens  may not be unrelated. It is possible
that the Kennedy opinion was the result of a long negotiation,
and that the price Justice Stevens exacted for not giving the
dissenters the crucial fourth vote needed to hear the case was
insertion of the language that can be read as warning the administration
not to presume on the court's patience.

The test may come if Mr. Padilla is acquitted by a jury in
the Miami federal case or receives and serves a short sentence.
The government would then have to decide whether to set him free
or find a way to keep him confined.

The federal court charges against him bear little if any relationship
to the accusations the administration made after he was arrested
after arriving at O'Hare International Airport in Chicago on
a flight from Pakistan. He was then described as an operative
for Al Qaeda on a mission to detonate a dirty bomb in the United
States.

In another development on Monday, the court agreed to resolve
a dispute among the lower courts with implications for thousands
of deportation and criminal sentencing cases. The question is
whether a drug offense that is only a misdemeanor under federal
law, but that an individual state's criminal code treats as a
felony, is deemed an "aggravated felony" for purposes
of immigration law or for adding time to a federal sentence.

The issue is particularly important in immigration law because
deportable aliens with "aggravated felonies" on their
records are ineligible for administrative discretion, making
their deportation essentially automatic, no matter the individual
circumstances. To resolve the issue, the court accepted two cases,
Lopez v. Gonzales, No. 05-547, and Toledo-Flores v. United States,
No. 05-7664.

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